Contacts of the helix formed by residues 341 - 368 (chain A) in PDB entry 2VIG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 5.8 7.2 - - - -
266A GLN 5.3 0.9 - - - -
269A ASP* 3.7 34.5 - - + -
270A MET* 4.0 10.5 - - + -
273A ILE* 3.8 21.5 - - + -
331A ALA* 3.8 17.5 - - - +
334A LEU* 3.8 9.6 - - + -
335A LYS* 3.6 39.7 - - + -
339A LYS 3.3 15.3 - - - -
340A PRO* 1.3 75.3 - - + +
342A ILE* 1.3 59.8 + - + +
344A GLU* 3.2 11.0 - - - -
345A ALA* 2.7 41.2 + - + +
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 6.3 1.3 - - + -
269A ASP* 3.5 40.6 - - + +
272A ARG* 5.4 0.7 + - - +
340A PRO* 3.9 4.1 - - + +
341A PHE* 1.3 77.8 - - + +
343A LYS* 1.3 67.1 + - - +
344A GLU* 3.7 0.4 + - - -
345A ALA* 4.0 2.1 - - - +
346A ALA* 3.1 23.6 + - - +
401A VAL* 3.7 14.4 - - + -
405A HIS* 3.3 42.6 - - + +
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 5.0 0.6 - - - +
342A ILE* 1.3 80.0 - - - +
344A GLU* 1.3 83.2 + - - +
346A ALA* 3.3 6.3 + - - +
347A MET* 2.9 52.9 + - + +
401A VAL* 5.1 1.3 - - - -
402A ILE* 4.0 18.3 - - + +
405A HIS* 3.9 30.1 - - + -
406A LEU* 4.5 15.5 - - + +
409A SER* 5.4 5.9 + - - +
322C GLU* 3.1 37.3 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU 4.4 2.6 - - - +
330A ARG* 3.7 40.4 + - - +
331A ALA* 3.8 13.7 - - + +
334A LEU* 3.4 34.0 - - + +
340A PRO 3.8 5.6 - - - +
341A PHE* 3.2 20.3 - - - +
342A ILE 3.7 0.5 + - - -
343A LYS* 1.3 97.5 + - - +
345A ALA* 1.3 62.0 + - - +
347A MET* 3.3 3.2 + - - +
348A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASP* 3.3 31.2 - - - +
272A ARG* 4.0 10.1 - - + +
273A ILE* 4.0 13.2 - - + -
331A ALA* 3.7 9.3 - - - +
341A PHE* 2.7 26.3 + - + +
342A ILE 4.0 2.7 - - - +
344A GLU* 1.3 74.0 - - - +
346A ALA* 1.3 55.4 + - - +
348A ALA* 3.4 3.8 + - - +
349A LYS* 3.0 30.3 + - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 4.8 5.5 - - - +
342A ILE 3.1 18.6 + - - +
343A LYS 3.5 4.5 - - - +
345A ALA* 1.3 74.9 - - - +
347A MET* 1.3 57.7 + - - +
349A LYS* 4.8 0.4 - - - -
350A LEU* 2.9 32.9 + - - +
398A GLN* 3.3 28.4 - - - +
401A VAL* 3.9 16.8 - - + -
402A ILE* 3.8 18.8 - - + -
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Residues in contact with MET 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.3 5.6 - - + -
330A ARG* 3.5 25.4 - - - +
343A LYS* 2.9 30.0 + - + +
344A GLU* 3.3 9.4 + - - +
346A ALA* 1.3 72.3 - - - +
348A ALA* 1.3 53.0 + - - +
350A LEU* 3.6 1.3 - - - +
351A ALA* 2.7 38.3 + - - +
402A ILE* 3.8 29.6 - - + -
318C ALA* 3.7 27.6 - - + -
319C LEU* 3.6 30.7 - - + +
322C GLU* 3.4 32.3 - - - +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG 5.5 0.2 - - - +
273A ILE* 5.8 1.8 - - - -
276A ALA* 3.6 7.4 - - + -
324A ALA 5.0 0.6 - - - +
327A LEU* 3.6 17.4 - - - +
328A THR* 3.6 35.5 + - - +
331A ALA* 4.7 2.2 - - + -
344A GLU 3.0 15.8 + - - +
345A ALA* 3.6 7.4 - - - +
347A MET* 1.3 76.9 - - - +
349A LYS* 1.3 57.7 + - - +
351A ALA* 4.1 0.4 - - - +
352A ALA* 2.9 35.0 + - - +
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.7 31.9 - - + +
275A ILE* 4.0 19.3 - - + -
276A ALA* 3.6 11.0 - - - +
345A ALA 3.0 17.6 + - - +
346A ALA 4.1 2.5 - - - +
348A ALA* 1.3 75.2 - - - +
350A LEU* 1.3 55.9 + - - +
352A ALA* 4.2 0.2 - - - +
353A SER* 2.7 40.6 + - - +
388A THR 2.6 27.9 + - - +
389A GLU* 3.9 10.7 + - - +
391A TYR 3.0 22.6 + - - -
392A GLU* 4.5 2.7 - - - -
393A GLY 2.8 23.4 + - - -
394A THR 4.5 2.4 - - - -
395A SER* 4.7 0.8 + - - +
398A GLN* 3.6 18.1 - - + +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA 2.9 19.6 + - - +
347A MET 3.6 3.1 - - - +
349A LYS* 1.3 77.9 - - - +
351A ALA* 1.3 62.8 + - - +
353A SER* 3.1 14.7 + - - -
354A GLU* 3.2 20.8 + - - +
395A SER* 3.8 25.6 - - - +
398A GLN* 4.0 9.2 - - + +
399A ARG* 3.6 55.4 - - + +
402A ILE* 3.8 18.6 - - + -
315C ALA* 6.0 0.7 - - + +
316C ASP* 4.8 1.8 - - - +
319C LEU* 3.8 19.5 - - + -
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 3.9 12.2 - - + +
327A LEU* 3.4 25.6 - - + -
347A MET 2.7 21.1 + - - +
348A ALA 4.1 1.6 - - - +
350A LEU* 1.3 74.0 - - - +
352A ALA* 1.3 57.4 + - - +
354A GLU* 4.0 3.3 - - - +
355A ALA* 3.0 30.5 + - - +
319C LEU* 4.3 13.0 - - + -
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 3.4 33.7 - - + +
279A ALA* 3.7 8.4 - - + +
280A LEU* 4.2 8.3 - - + +
283A ALA* 5.3 0.5 - - - +
324A ALA* 3.7 18.8 - - + +
328A THR* 4.7 0.9 - - - +
348A ALA 2.9 19.2 + - - +
351A ALA* 1.3 74.1 - - - +
353A SER* 1.3 55.9 + - - +
355A ALA* 3.2 3.4 + - - +
356A ALA* 2.8 36.2 + - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 3.9 4.5 - - - +
349A LYS* 2.7 26.7 + - - +
350A LEU* 3.1 8.5 + - - -
352A ALA* 1.3 77.4 - - - +
354A GLU* 1.3 65.7 + - - +
356A ALA 3.5 0.2 + - - -
357A THR* 3.2 17.5 + - - -
388A THR* 3.2 52.3 + - - -
389A GLU* 3.7 17.7 - - - +
395A SER* 4.4 3.3 + - - -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.2 24.3 + - + +
351A ALA* 4.3 3.7 - - - +
353A SER* 1.3 86.2 + - - +
355A ALA* 1.3 57.2 + - - +
357A THR* 3.5 2.8 + - - +
358A ALA* 3.0 29.9 + - - +
389A GLU* 3.6 20.8 - - - +
395A SER* 3.9 9.8 + - - +
399A ARG* 3.1 41.1 + - - -
319C LEU* 5.9 1.2 - - - +
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 5.2 2.2 - - + -
320A ALA* 3.9 30.3 - - + +
321A LEU* 4.9 1.3 - - + -
324A ALA* 4.6 2.0 - - + -
351A ALA 3.0 19.9 + - - +
352A ALA* 3.6 7.0 - - - +
354A GLU* 1.3 74.3 - - - +
356A ALA* 1.3 55.5 + - - +
358A ALA* 4.5 4.7 - - - +
359A ILE* 2.7 55.4 + - + +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ALA* 3.6 28.9 - - + +
282A ILE* 4.5 2.1 - - + +
283A ALA* 3.9 17.8 - - + +
352A ALA 2.8 20.1 + - - +
353A SER 3.7 5.4 - - - +
354A GLU 3.4 0.2 - - - -
355A ALA* 1.3 71.8 - - - +
357A THR* 1.3 57.9 - - - +
359A ILE* 4.0 0.5 - - - +
360A SER* 3.0 32.7 + - - -
385A ALA* 3.5 17.9 - - + +
388A THR* 4.4 2.7 - - - +
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Residues in contact with THR 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A SER 3.2 9.9 + - - -
354A GLU 3.9 2.7 - - - +
356A ALA* 1.3 76.7 - - - +
358A ALA* 1.3 62.9 + - - +
360A SER* 3.1 7.6 + - - -
361A HIS* 3.0 29.7 + - + +
382A TYR* 4.3 3.4 + - + -
385A ALA* 3.7 20.9 + - - +
386A ARG* 3.8 4.3 + - - -
389A GLU* 2.8 31.8 + - - +
361B HIS* 3.8 15.3 - - + +
382B TYR* 3.9 14.3 + - - +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A MET* 5.7 0.2 - - - -
354A GLU 3.0 17.9 + - - +
355A ALA* 3.9 4.9 - - - +
357A THR* 1.3 74.6 - - - +
359A ILE* 1.3 67.3 + - + +
361A HIS* 3.4 5.5 + - - +
362A GLN* 3.0 29.7 + - + +
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 3.5 42.6 - - + +
286A ALA* 3.9 9.0 - - + -
287A LEU* 4.0 5.6 - - + +
317A MET* 3.5 59.7 - - + +
320A ALA* 4.4 4.0 - - + -
321A LEU* 3.9 13.5 - - + +
355A ALA* 2.7 36.9 + - + +
356A ALA 4.2 1.6 - - - +
358A ALA* 1.3 73.5 - - + +
360A SER* 1.3 56.9 + - - +
362A GLN 3.4 0.9 + - - -
363A ALA* 2.9 26.5 + - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 5.3 1.3 - - - -
286A ALA* 4.1 12.8 - - - -
356A ALA 3.0 21.2 + - - -
357A THR* 3.1 9.5 + - - -
359A ILE* 1.3 74.5 - - - +
361A HIS* 1.3 67.9 + - - +
363A ALA* 3.4 2.6 + - - +
364A ILE* 3.1 27.5 + - - +
378A ALA 4.7 1.3 - - - +
381A HIS* 3.8 14.6 - - - -
382A TYR* 3.3 40.5 - - - +
385A ALA* 3.8 2.4 - - - +
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Residues in contact with HIS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A THR* 3.0 20.9 + - + +
358A ALA* 3.6 7.2 - - - +
360A SER* 1.3 79.5 + - - +
362A GLN* 1.3 78.7 + - - +
364A ILE* 3.3 1.3 + - - +
365A GLN* 3.1 11.0 + - - -
382A TYR* 3.6 28.5 - + + -
357B THR* 3.8 10.9 - - + +
386B ARG* 2.9 55.1 + - - +
389B GLU* 2.8 37.0 + - - -
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 2.8 43.6 + - + +
317A MET* 3.9 25.4 - - + -
358A ALA* 3.0 22.1 + - + +
359A ILE 3.9 0.9 - - - +
361A HIS* 1.3 105.9 + - - +
363A ALA* 1.3 58.1 + - - +
365A GLN* 3.7 9.6 - - - +
366A ILE* 3.0 36.2 + - + +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ALA* 3.5 30.1 - - + +
289A CYS* 5.4 1.3 - - - -
290A ALA* 3.9 15.9 - - + +
317A MET* 4.0 0.8 - - + +
359A ILE 2.9 20.7 + - - +
360A SER* 3.6 8.7 - - - +
361A HIS 3.3 0.2 - - - -
362A GLN* 1.3 68.7 - - - +
364A ILE* 1.3 67.5 + - - +
366A ILE* 3.4 1.6 + - - +
367A LEU* 3.2 30.6 + - + +
378A ALA* 4.4 12.6 - - + -
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Residues in contact with ILE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER 3.1 10.1 + - - +
361A HIS 3.5 7.2 - - - +
363A ALA* 1.3 76.7 - - - +
365A GLN* 1.3 63.3 + - - +
367A LEU* 3.1 3.8 + - - +
368A GLY 3.1 21.1 + - - +
371A GLY* 3.6 33.0 - - - +
372A TYR* 4.9 1.6 - - - -
378A ALA* 3.9 14.3 - - + +
379A GLU* 4.0 11.4 - - - -
382A TYR* 3.6 42.6 - - + -
231B LEU* 4.3 8.1 - - + -
386B ARG* 3.5 25.1 - - + +
390B ILE* 4.0 12.5 - - + +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 4.4 5.2 - - - +
361A HIS* 3.1 12.2 + - - +
362A GLN* 3.3 21.5 + - - +
363A ALA 3.3 0.6 - - - -
364A ILE* 1.3 75.0 - - - +
366A ILE* 1.3 59.0 + - - +
368A GLY* 3.1 12.1 + - - -
386B ARG* 2.9 33.9 + - - +
389B GLU* 3.0 29.1 + - - +
390B ILE* 3.8 7.3 - - - +
394B THR* 3.8 6.5 - - - +
395B SER* 3.6 12.4 + - - +
396B GLU* 3.0 38.8 + - - +
501B FAD 2.8 22.3 + - - +
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA* 3.9 16.8 - - + +
293A TYR* 3.9 0.9 - - - -
294A ALA* 3.8 28.7 - - + +
304A LEU* 3.6 12.8 - - + +
310A ILE* 4.0 10.8 - - + +
313A LYS* 3.8 29.2 - - + -
314A LEU* 3.7 29.6 - - + -
317A MET* 3.9 14.6 - - - -
362A GLN 3.0 21.0 + - - +
363A ALA 3.9 3.6 - - - +
364A ILE 3.3 0.2 - - - -
365A GLN* 1.3 74.3 - - - +
367A LEU* 1.3 61.6 + - + +
501B FAD 3.0 30.8 - - - +
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A CYS* 4.1 6.5 - - - +
290A ALA* 4.2 15.5 - - - -
293A TYR* 3.6 56.6 + - + -
363A ALA 3.2 12.8 + - - +
364A ILE 3.1 3.4 + - - +
366A ILE* 1.3 76.8 - - + +
368A GLY* 1.3 62.4 + - - +
369A GLY 3.3 2.6 + - - -
370A MET* 3.4 9.0 + - + +
371A GLY* 3.4 20.2 - - - +
376A MET* 3.6 42.6 - - + -
378A ALA* 3.9 20.0 - - + -
501B FAD 4.2 5.9 + - - +
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE 3.1 5.5 + - - +
365A GLN 3.1 17.1 + - - -
366A ILE 3.2 0.8 + - - -
367A LEU* 1.3 77.0 - - - +
369A GLY* 1.3 58.3 + - - -
371A GLY* 2.9 19.4 + - - -
372A TYR 3.8 2.4 + - - -
390B ILE* 3.8 22.7 - - - +
394B THR* 5.2 1.8 - - - -
501B FAD 3.8 20.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il